Environmental filtering mediates desert ant community assembly at two spatial scales

Understanding the mechanisms that maintain species coexistence and determine patterns of community assembly are fundamental goals of ecology. Quantifying the relationship between species traits and stress gradients is a necessary step to disentangle assembly processes and to be able to predict the outcome of environmental change. We examined the hypothesis that desert ant communities are assembled by niche-based processes i.e., environmental filtering and limiting similarity. First, we used population-level morphological trait measurements to study the functional structure of ant communities along a dryland environmental stress gradient. Second, we developed species distribution models for each species to quantify large-scale climatic niche overlap between species. Body, femur, antennal scape, and head lengths were correlated with environmental gradients. Regionally, the ant community was significantly and functionally overdispersed in terms of morphological traits which suggests the importance of competition to ant community structure. Ant community assembly was also strongly influenced by environmental factors as the degree of functional trait divergence, but not phylogenetic divergence, decreased with increasing environmental stress. Thus, environmental stress likely mediates limiting similarity in these desert ecosystems. Species with lower climatic niche overlap were more dissimilar in morphological traits. This suggests that environmental filtering on ant functional traits is important at the scale of species distributions in addition to regional scales. This study shows that environmental and biotic filtering (i.e., niche-based assembly mechanisms) are jointly and non-independently structuring the ant community.

Taxonomic accuracy and complementarity between bulk and eDNA metabarcoding provides an alternative to morphology for biological assessment of freshwater macroinvertebrates

Determining biological status of freshwater ecosystems is critical for ensuring ecosystem health and maintaining associated services to such ecosystems. Freshwater macroinvertebrates respond predictably to environmental disturbances and are widely used in biomonitoring programs. However, many freshwater species are difficult to capture and sort from debris or substrate and morphological identification is challenging, especially larval stages, damaged specimens, or hyperdiverse groups such as Diptera. The advent of high throughput sequencing technologies has enhanced DNA barcoding tools to automatise species identification for whole communities, as metabarcoding is increasingly used to monitor biodiversity. However, recent comparisons have revealed little congruence between morphological and molecular-based identifications. Using broad range universal primers for DNA barcode marker cox1, we compare community composition captured between morphological and molecular-based approaches from different sources - tissue-based (bulk benthic and bulk drift samples) and environmental DNA (eDNA, filtered water) metabarcoding - for samples collected along a gradient of anthropogenic disturbances. For comparability, metabarcoding taxonomic assignments were filtered by taxa included in the standardised national biological metric IBMWP. At the family level, bulk benthic metabarcoding showed the highest congruence with morphology, and the most abundant taxa were captured by all techniques. Richness captured by morphology and bulk benthic metabarcoding decreased along the gradient, whereas richness recorded by eDNA remained constant and increased downstream when sequencing bulk drift. Estimates of biological metrics were higher using molecular than morphological identification. At species level, diversity captured by bulk benthic samples were higher than the other techniques. Importantly, bulk benthic and eDNA metabarcoding captured different and complementary portions of the community - benthic versus water column, respectively - and their combined use is recommended. While bulk benthic metabarcoding can likely replace morphology using similar benthic biological indices, water eDNA will require new metrics because this technique sequences a different portion of the community.

Vegetation structure drives mosquito community composition in UK's largest managed lowland wetland

PURPOSE

The rising burden of mosquito-borne diseases in Europe extends beyond urban areas, encompassing rural and semi-urban regions near managed and natural wetlands evidenced by recent outbreaks of Usutu and West Nile viruses. While wetland management policies focus on biodiversity and ecosystem services, few studies explore the impact on mosquito vectors.

METHODS

Our research addresses this gap, examining juvenile mosquito and aquatic predator communities in 67 ditch sites within a South England coastal marsh subjected to different wetland management tiers. Using joint distribution models, we analyse how mosquito communities respond to abiotic and biotic factors influenced by wetland management.

RESULTS

Of the 12 mosquito species identified, Culiseta annulata (Usutu virus vector) and Culex pipiens (Usutu and West Nile virus vector) constitute 47% of 6825 larval mosquitoes. Abundant predators include Coleoptera (water beetles) adults, Corixidae (water boatmen) and Zygoptera (Damselfy) larvae. Models reveal that tier 3 management sites (higher winter water levels, lower agricultural intensity) associated with shade and less floating vegetation are preferred by specific mosquito species. All mosquito species except Anopheles maculipennis s.l., are negatively impacted by potential predators. Culiseta annulata shows positive associations with shaded and turbid water, contrary to preferences of Corixidae predators.

CONCLUSIONS

Tier 3 areas managed for biodiversity, characterised by higher seasonal water levels and reduced livestock grazing intensity, provide favourable habitats for key mosquito species that are known vectors of arboviruses, such as Usutu and West Nile. Our findings emphasise the impact of biodiversity-focused wetland management, altering mosquito breeding site vegetation to enhance vector suitability. Further exploration of these trade-offs is crucial for comprehending the broader implications of wetland management.

Plant networks are more connected by invasive brome and native shrub facilitation in Central California drylands

Dominant vegetation in many ecosystems is an integral component of structure and habitat. In many drylands, native shrubs function as foundation species that benefit other plants and animals. However, invasive exotic plant species can comprise a significant proportion of the vegetation. In Central California drylands, the facilitative shrub Ephedra californica and the invasive Bromus rubens are widely dispersed and common. Using comprehensive survey data structured by shrub and open gaps for the region, we compared network structure with and without this native shrub canopy and with and without the invasive brome. The presence of the invasive brome profoundly shifted the network measure of centrality in the microsites structured by a shrub canopy (centrality scores increased from 4.3 under shrubs without brome to 6.3, i.e. a relative increase of 42%). This strongly suggests that plant species such as brome can undermine the positive and stabilizing effects of native foundation plant species provided by shrubs in drylands by changing the frequency that the remaining species connect to one another. The net proportion of positive and negative associations was consistent across all microsites (approximately 50% with a total of 14% non-random co-occurrences on average) suggesting that these plant-plant networks are rewired but not more negative. Maintaining resilience in biodiversity thus needs to capitalize on protecting native shrubs whilst also controlling invasive grass species particularly when associated with shrubs.

Comprehensive insights into the differences of fungal communities at taxonomic and functional levels in stony coral Acropora intermedia under a natural bleaching event

Previous studies have reported the correlations between bacterial communities and coral bleaching, but the knowledge of fungal roles in coral bleaching is still limited. In this study, the taxonomic and functional diversities of fungi in unbleached, partly bleached and bleached stony coral Acropora intermedia were investigated through the ITS-rRNA gene next-generation sequencing. An unexpected diversity of successfully classified fungi (a total of 167 fungal genera) was revealed in this study, and the partly bleached coral samples gained the highest fungal diversity, followed by bleached and unbleached coral samples. Among these fungi, 122 genera (nearly 73.2%) were rarely found in corals in previous studies, such as Calostoma and Morchella, which gave us a more comprehensive understanding of coral-associated fungi. Positively correlated fungal genera (Calostoma, Corticium, Derxomyces, Fusicolla, Penicillium and Vishniacozyma) and negative correlated fungal genera (Blastobotrys, Exophiala and Dacryopinax) with the coral bleaching were both detected. It was found that a series of fungal genera, dominant by Apiotrichum, a source of opportunistic infections, was significantly enriched; while another fungal group majoring in Fusicolla, a probiotic fungus, was distinctly depressed in the bleached coral. It was also noteworthy that the abundance of pathogenic fungi, including Fusarium, Didymella and Trichosporon showed a rising trend; while the saprotrophic fungi, including Tricladium, Botryotrichum and Scleropezicula demostrated a declining trend as the bleaching deteriorating. The rising of pathogenic fungi and the declining of saprotrophic fungi revealed the basic rules of fungal community transitions in the coral bleaching, but the mechanism of coral-associated fungal interactions still lacks further investigation. Overall, this is an investigation focused on the differences of fungal communities at taxonomic and functional levels in stony coral A. intermedia under different bleaching statuses, which provides a better comprehension of the correlations between fungal communities and the coral bleaching.

Sympatry in a nightingale contact zone has no effect on host-specific blood parasite prevalence and lineage diversity

Parasites are a key driving force behind many ecological and evolutionary processes. Prevalence and diversity of parasites, as well as their effects on hosts, are not uniform across host species. As such, the potential parasite spillover between species can significantly influence outcomes of interspecific interactions. We screened two species of Luscinia nightingales for haemosporidian blood parasites (Plasmodium, Leucocytozoon and Haemoproteus) along an approximately 3000 km transect in Europe, incorporating areas of host distant allopatry, close allopatry and sympatry. We found significant differences in infection rates between the two host species, with common nightingales having much lower parasite prevalence than thrush nightingales (36.7% versus 83.8%). This disparity was mostly driven by Haemoproteus prevalence, which was significantly higher in thrush nightingales while common nightingales had a small, but significantly higher, Plasmodium prevalence. Furthermore, we found no effect of proximity to the contact zone on infection rate in either host species. Despite having lower infection prevalence, common nightingales were infected with a significantly higher diversity of parasite lineages than thrush nightingales, and lineage assemblages differed considerably between the two species, even in sympatry. This pattern was mostly driven by the large diversity of comparatively rare lineages, while the most abundant lineages were shared between the two host species. This suggests that, despite the close evolutionary relationships between the two nightingales, there are significant differences in parasite prevalence and diversity, regardless of the distance from the contact zone. This suggests that spillover of haemosporidian blood parasites is unlikely to contribute towards interspecific interactions in this system.

Environmental drivers of biogeography and community structure in a Mid-Atlantic estuary

Estuaries include some of the most productive yet anthropogenically impacted marine ecosystems on the planet, and provide critical habitat to many ecologically and economically important marine species. In order to elucidate ecological function in estuaries, we must understand what factors drive community dynamics. Delaware Bay is the third largest estuary in the United States and hosts over 200 species of migrant and resident fishes and invertebrates. The Delaware Division of Fish and Wildlife has conducted two long-term trawl surveys at monthly intervals in Delaware Bay since 1966. The two surveys collect data on environmental conditions, species composition, and number of fishes and macroinvertebrates across different size classes and life histories. Using a suite of multivariate approaches including hierarchical cluster analysis, canonical correlation analysis, and permutational multivariate analysis of variance, we characterized the fish and macroinvertebrate community in Delaware Bay and found that community composition and environmental conditions varied across spatial and seasonal scales. We identified four distinct biogeographic regions, based on environmental conditions and community composition, which were consistent across surveys. We found that the community was driven primarily by gradients in temperature and salinity and that abundant, frequently occurring species in the Bay have well-defined environmental associations. Our work represents the first attempt to use an existing historical survey to better understand how environmental parameters influence diversity and distribution of macrofauna within Delaware Bay, providing insight into how abiotic variables, influenced by climate, may impact the Delaware Bay ecosystem and similar estuarine ecosystems worldwide.

Plant-endophyte communication: Scaling from molecular mechanisms to ecological outcomes

Diverse communities of fungal endophytes reside in plant tissues, where they affect and are affected by plant physiology and ecology. For these intimate interactions to form and persist, endophytes and their host plants engage in intricate systems of communication. The conversation between fungal endophytes and plant hosts ultimately dictates endophyte community composition and function and has cascading effects on plant health and plant interactions. In this review, we synthesize our current knowledge on the mechanisms and strategies of communication used by endophytic fungi and their plant hosts. We discuss the molecular mechanisms of communication that lead to organ specificity of endophytic communities and distinguish endophytes, pathogens, and saprotrophs. We conclude by offering emerging perspectives on the relevance of plant-endophyte communication to microbial community ecology and plant health and function.

Elucidating potential bioindicators from insights in the diversity and assembly processes of prokaryotic and eukaryotic communities in the Mekong River

Drivers for spatio-temporal distribution patterns of overall planktonic prokaryotes and eukaryotes in riverine ecosystems are generally not fully understood. This study employed amplicon metabarcoding to investigate the distributions and assembly mechanisms of bacterial and eukaryotic communities in the Mekong River. The prevailing bacteria taxa were found to be Betaproteobacteria, Actinobacteria, and Bacteroidetes, while the dominant eukaryotic organisms were cryptophytes, chlorophytes, and diatoms. The community assemblages were influenced by a combination of stochastic and deterministic processes. Drift (DR) and dispersal limitation (DL), signifying the stochastic mechanism, were the main processes shaping the overall prokaryotic and eukaryotic communities. However, homogeneous selection (HoS), indicating deterministic mechanism, played a major role in the assembly process of core prokaryotic communities, especially in the wet season. In contrast, the core eukaryotic communities including Opisthokonta, Sar, and Chlorophyta were dominated by stochastic processes. The significance of HoS within prokaryotic communities was also found to exhibit a decreasing trend from the upstream sampling sites (Chiang Saen and Chiang Khan, Nong Khai) towards the downstream sites (Mukdahan, and Khong Chiam) of the Mekong River. The environmental gradients resulting from the site-specific variations and the gradual decrease in elevation along the river may have a potential influence on the role of HoS in community assembly. Crucial environmental factors that shape the phylogenetic structure within distinct bins of the core prokaryotic communities including water depth, temperature, chloride, sodium, and sulphate were identified, as inferred by their correlation with the beta Net Relatedness Index (betaNRI) during the wet season. Overall, these findings enhance understanding of the complex mechanisms governing the spatio-temporal dynamics of prokaryotic and eukaryotic communities in the Mekong River. Finally, insights gained from this study could provide information on further use of specific core bacteria as microbial-based bioindicators that are effective for the assessment and conservation of the Mekong River ecosystem.

Promoting Bird Functional Diversity on Landscapes with a Matrix of Planted Eucalyptus spp. in the Atlantic Forest

Promoting the diversity of biological communities in areas of agricultural production is a very current debate since protected areas may not be sufficient to ensure biodiversity conservation. Among the biological communities affected by the production areas are birds, which show rapid responses to changes in the landscape. Here we seek to understand how landscape planning, concerning its composition and configuration, in areas with a matrix of planted Eucalyptus spp. forests influences the functional diversity of bird assemblages in the Atlantic Forest. Our results show that the spatial distribution design of planted forests in terms of age, land cover and clone types have effects on bird diversity with regard to functional divergence, functional evenness and species richness. These results reinforce the importance of good management for the maintenance of bird diversity. We found that bird functional diversity in planted forest matrices increased with the proximity index, proportion of native vegetation and age importance value, and is negatively influenced by edge density and proportion of forest plantation. For bird conservation, it is thus better to associate Eucalyptus spp. with other cover types in the landscape. These results corroborate that, to increase bird functional diversity, it is possible to associate conservation and production in the same landscape. Mosaic landscapes have great potential to contribute to the conservation of bird biodiversity outside protected areas. However, decisions regarding the management of planted forests and planning of improved areas intended for conservation seem to be decisive to ensure the maintenance of bird biodiversity.

Distribution of Culex pipiens life stages across urban green and grey spaces in Leiden, The Netherlands

BACKGROUND

There is an urgent need for cities to become more climate resilient; one of the key strategies is to include more green spaces in the urban environment. Currently, there is a worry that increasing green spaces might increase mosquito nuisance. As such, this study explores a comprehensive understanding of how mosquitoes utilise contrasting grey and green habitats at different life stages and which environmental factors could drive these distributions.

METHODS

We used a setup of six paired locations, park (green) vs. residential (grey) areas in a single model city (Leiden, The Netherlands), where we sampled the abundances of different mosquito life stages (eggs, larvae, adults) and the local microclimatic conditions. In this study, we focused on Culex pipiens s.l., which is the most common and abundant mosquito species in The Netherlands.

RESULTS

Our results show that while Cx. pipiens ovipositioning rates (number of egg rafts) and larval life stages were far more abundant in residential areas, adults were more abundant in parks. These results coincide with differences in the number of suitable larval habitats (higher in residential areas) and differences in microclimatic conditions (more amenable in parks).

CONCLUSIONS

These findings suggest that Cx. pipiens dispersal may be considerably more important than previously thought, where adult Cx. pipiens seek out the most suitable habitat for survival and breeding success. Our findings can inform more targeted and efficient strategies to mitigate and reduce mosquito nuisance while urban green spaces are increased, which make cities more climate resilient.

Bird Fauna Composition in a Protected Area in Southern Brazil

The integrity of natural landscapes is affected by human actions, mainly by the intensification and expansion of agriculture. Factors such as fragment size and the structure of the environment can determine changes in the structure and composition of bird assemblages. In this study we evaluated the bird species composition in three structurally different forest environments, defined as the Core areas, Edge areas, and Buffer areas. The surveys were performed in the Natural Park of Sertão (NPS) and its surroundings in the southern limit of the Atlantic Forest, southern Brazil. To record species composition of birds, the point count method was used. The bird species were categorized according to feeding habits, habitat use, and sensitivity to forest fragmentation. A total of 131 species of birds distributed in 18 orders and 38 families were recorded. The species composition varied between the three areas and there was a significant difference in diversity between the Core and Edge areas and the Core and Buffer areas. Omnivorous species were found more in the Buffer areas than in the Core areas. Species that use the Broad habitat were more frequent in the Buffer and Edge areas than in the Core areas. Species that use the Forest habitat were found more in the Core areas than in the Buffer areas. Most recorded species (66%) have low sensitivity to forest fragmentation. The assemblage patterns found in this study, notably the differences among the three areas in diversity and species composition, can be explained by the ecological traits and the sensitivity levels of birds to forest fragmentation, which in turn seem to reflect different forest structures in the NPS and its surroundings. Although the Edge and Buffer areas have greater diversity, the Core areas showed great importance in maintaining species that are more sensitive to forest fragmentation. Even the largest fragments (such as the NPS), considering the regional context, may have bird species that are widely distributed and less sensitive to forest fragmentation. Forested habitat species may no longer occur or be restricted to the core area of the fragments. For conservation of bird fauna in the NPS, the maintenance of the core areas is essential, especially for those species that require a structurally preserved environment.

Geographic range size and species morphology determines the organization of sponge host-guest interaction networks across tropical coral reefs

Sponges are widely spread organisms in the tropical reefs of the American Northwest-Atlantic Ocean, they structure ecosystems and provide services such as shelter, protection from predators, and food sources to a wide diversity of both vertebrates and invertebrates species. The high diversity of sponge-associated fauna can generate complex networks of species interactions over small and large spatial-temporal gradients. One way to start uncovering the organization of the sponge host-guest complex networks is to understand how the accumulated geographic area, the sponge morphology and, sponge taxonomy contributes to the connectivity of sponge species within such networks. This study is a meta-analysis based on previous sponge host-guest literature obtained in 65 scientific publications, yielding a total of 745 host-guest interactions between sponges and their associated fauna across the Caribbean Sea and the Gulf of Mexico. We analyzed the sponge species contribution to network organization in the Northwest Tropical Atlantic coral reefs by using the combination of seven complementary species-level descriptors and related this importance with three main traits, sponge-accumulated geographic area, functional sponge morphology, and sponges' taxonomy bias. In general, we observed that sponges with a widespread distribution and a higher accumulated geographic area had a greater network structural contribution. Similarly, we also found that Cup-like and Massive functional morphologies trend to be shapes with a greater contribution to the interaction network organization compared to the Erect and Crust-like morphos. Lastly, we did not detect a taxonomy bias between interaction network organization and sponges' orders. These results highlight the importance of a specific combination of sponge traits to promote the diversity of association between reef sponges and their guest species.

Behavioral dominance interactions between two species of burying beetles (Nicrophorus orbicollis and Nicrophorus pustulatus)

Closely related species with ecological similarity often aggressively compete for a common, limited resource. This competition is usually asymmetric and results in one species being behaviorally dominant over the other. Trade-offs between traits for behavioral dominance and alternative strategies can result in different methods of resource acquisition between the dominant and subordinate species, with important consequences for resource partitioning and community structure. Body size is a key trait thought to commonly determine behavioral dominance. Priority effects (i.e., which species arrives at the resource first), however, can also determine the outcome of interactions, as can species-specific traits besides size that give an advantage in aggressive contests (e.g., weapons). Here, we test among these three alternative hypotheses of body size, priority effects, and species identity for what determines the outcome of competitive interactions among two species of burying beetles, Nicrophorus orbicollis and N. pustulatus. Both overlap in habitat and seasonality and exhibit aggressive competition over a shared breeding resource of small vertebrate carrion. In trials, we simulated what would happen upon the beetles' discovery of a carcass in nature by placing a carcass and one beetle of each species in a container and observing interactions over 13 h trials (n = 17 trials). We recorded and categorized interactions between beetles and the duration each individual spent in contact with the carcass (the key resource) to determine which hypothesis predicted trial outcomes. Body size was our only significant predictor; the largest species won most aggressive interactions and spent more time in contact with the carcass. Our results offer insight into the ecology and patterns of resource partitioning of N. orbicollis and N. pustulatus, the latter of which is unique among local Nicrophorus for being a canopy specialist. N. pustulatus is also unique among all Nicrophorus in using snake eggs, in addition to other carrion, as a breeding resource. Our results highlight the importance of body size and related trade-offs in ecology and suggest parallels with other coexisting species and communities.

Arable plant communities as a surrogate of crop rhizosphere microbiota

Soil microbiota is a crucial component of agroecosystem biodiversity, enhancing plant growth and providing important services in agriculture. However, its characterization is demanding and relatively expensive. In this study, we evaluated whether arable plant communities can be used as a surrogate of bacterial and fungal communities of the rhizosphere of Elephant Garlic (Allium ampeloprasum L.), a traditional crop plant of central Italy. We sampled plant, bacterial, and fungal communities, i.e., the groups of such organisms co-existing in space and time, in 24 plots located in eight fields and four farms. At the plot level, no correlations in species richness emerged, while the composition of plant communities was correlated with that of both bacterial and fungal communities. As regards plants and bacteria, such correlation was mainly driven by similar responses to geographic and environmental factors, while fungal communities seemed to be correlated in species composition with both plants and bacteria due to biotic interactions. All the correlations in species composition were unaffected by the number of fertilizer and herbicide applications, i.e., agricultural intensity. Besides correlations, we detected a predictive relationship of plant community composition towards fungal community composition. Our results highlight the potential of arable plant communities to be used as a surrogate of crop rhizosphere microbial communities in agroecosystems.

Lemur Gut Microeukaryotic Community Variation Is Not Associated with Host Phylogeny, Diet, or Habitat

Identifying the major forces driving variation in gut microbiomes enhances our understanding of how and why symbioses between hosts and microbes evolved. Gut prokaryotic community variation is often closely associated with host evolutionary and ecological variables. Whether these same factors drive variation in other microbial taxa occupying the animal gut remains largely untested. Here, we present a one-to-one comparison of gut prokaryotic (16S rRNA metabarcoding) and microeukaryotic (18S rRNA metabarcoding) community patterning among 12 species of wild lemurs. Lemurs were sampled from dry forests and rainforests of southeastern Madagascar and display a range of phylogenetic and ecological niche diversity. We found that while lemur gut prokaryotic community diversity and composition vary with host taxonomy, diet, and habitat, gut microeukaryotic communities have no detectable association with any of these factors. We conclude that gut microeukaryotic community composition is largely random, while gut prokaryotic communities are conserved among host species. It is likely that a greater proportion of gut microeukaryotic communities comprise taxa with commensal, transient, and/or parasitic symbioses compared with gut prokaryotes, many of which form long-term relationships with the host and perform important biological functions. Our study highlights the importance of greater specificity in microbiome research; the gut microbiome contains many "omes" (e.g., prokaryome, eukaryome), each comprising different microbial taxa shaped by unique selective pressures.

Community composition drives siderophore dynamics in multispecies bacterial communities

BACKGROUND

Intraspecific public goods are commonly shared within microbial populations, where the benefits of public goods are largely limited to closely related conspecifics. One example is the production of iron-scavenging siderophores that deliver iron to cells via specific cell envelope receptor and transport systems. Intraspecific social exploitation of siderophore producers is common, since non-producers avoid the costs of production but retain the cell envelope machinery for siderophore uptake. However, little is known about how interactions between species (i.e., interspecific interactions) can shape intraspecific public goods exploitation. Here, we predicted that strong competition for iron between species in diverse communities will increase costs of siderophore cooperation, and hence drive intraspecific exploitation. We examined how increasing microbial community species diversity shapes intraspecific social dynamics by monitoring the growth of siderophore producers and non-producers of the plant-growth promoting bacterium Pseudomonas fluorescens, embedded within tree-hole microbial communities ranging from 2 to 15 species.

RESULTS

We find, contrary to our prediction, that siderophore production is favoured at higher levels of community species richness, driven by increased likelihood of encountering key species that reduce the growth of siderophore non-producing (but not producing) strains of P. fluorescens.

CONCLUSIONS

Our results suggest that maintaining a diverse soil microbiota could partly contribute to the maintenance of siderophore production in natural communities.

Diversity and composition of mixed-ploidy unisexual salamander assemblages reflect the key influence of host species

Understanding processes that govern and sustain biological diversity is a central goal of community ecology. Unisexual complexes, where reproduction depends on sperm from males of one or more bisexual host species, are rare and the processes driving their diversity and structure remain poorly understood. Unisexual Ambystoma salamanders produce distinct biotypes ('genomotypes') depending on which bisexual species they 'steal' sperm from. This reproductive mode should generate distinct assemblages depending on the locally available bisexual host species. Yet, how availability and relative abundance of multiple bisexual hosts influences composition and diversity of natural unisexual assemblages at local or regional scales remains unknown. We hypothesize that host identity most directly drives local assemblage composition, with host variation associated with increased beta and gamma diversity within unisexuals. We collected genetic samples from Ambystoma salamanders across Pelee Island, Ontario, Canada (2015-2022). Two host species were identified (A. texanum and A. laterale) with nine sites having a single host and one site having both. Unisexual assemblages were grouped into four clusters by similarity, with host identity being a key determinant. Gamma diversity increased as a result of distinct host-specific assemblages forming at different sites on the island (i.e., high beta diversity). Assemblage composition, but not diversity, was correlated with relative host abundance, which may reflect matching niche requirements between host and unisexual forms they produce. Our results demonstrate that diversity and structure of unisexual assemblages are clearly shaped by their host(s) and such systems may serve as models for studying how biotic interactions shape ecological communities.

Assembly processes and functional diversity of marine protists and their rare biosphere

BACKGROUND

The mechanisms shaping the rare microbial biosphere and its role in ecosystems remain unclear. We developed an approach to study ecological patterns in the rare biosphere and use it on a vast collection of marine microbiomes, sampled in coastal ecosystems at a regional scale. We study the assembly processes, and the ecological strategies constituting the rare protistan biosphere. Using the phylogeny and morpho-trophic traits of these protists, we also explore their functional potential.

RESULTS

Taxonomic community composition remained stable along rank abundance curves. Conditionally rare taxa, driven by selection processes, and transiently rare taxa, with stochastic distributions, were evidenced along the rank abundance curves of all size-fractions. Specific taxa within the divisions Sagenista, Picozoa, Telonemia, and Choanoflagellida were rare across time and space. The distribution of traits along rank abundance curves outlined a high functional redundancy between rare and abundant protists. Nevertheless, trophic traits illustrated an interplay between the trophic groups of different size-fractions.

CONCLUSIONS

Our results suggest that rare and abundant protists are evolutionary closely related, most notably due to the high microdiversity found in the rare biosphere. We evidenced a succession of assembly processes and strategies of rarity along rank abundance curves that we hypothesize to be common to most microbiomes at the regional scale. Despite high functional redundancy in the rare protistan biosphere, permanently rare protists were evidenced, and they could play critical functions as bacterivores and decomposers from within the rare biosphere. Finally, changes in the composition of the rare protistan biosphere could be influenced by the trophic regime of aquatic ecosystems. Our work contributes to understanding the role of rare protists in microbiomes.

Changes in Coleopteran assemblages over a successional chronosequence in a Mexican tropical dry forest

Coleopterans are the most diverse animal group on Earth and constitute good indicators of environmental change. However, little information is available about Coleopteran communities' responses to disturbance and land-use change. Tropical dry forests have undergone especially extensive anthropogenic impacts in the past decades. This has led to mosaic landscapes consisting of areas of primary forest surrounded by pastures, agricultural fields and secondary forests, which negatively impacts many taxonomic groups. However, such impacts have not been assessed for most arthropod groups. In this work, we compared the abundance, richness and diversity of Coleopteran morphospecies in four different successional stages in a tropical dry forest in western Mexico, to answer the question: How do Coleopteran assemblages associate with vegetation change over the course of forest succession? In addition, we assessed the family composition and trophic guilds for the four successional stages. We found 971 Coleopterans belonging to 107 morphospecies distributed in 28 families. Coleopteran abundance and richness were greatest for pastures than for latter successional stages, and the most abundant family was Chrysomelidae, with 29% of the individuals. Herbivores were the most abundant guild, accounting for 57% of the individuals, followed by predators (22%) and saprophages (21%) beetles. Given the high diversity and richness found throughout the successional chronosequence of the studied tropical dry forest, in order to have the maximum number of species associated with tropical dry forests, large tracts of forest should be preserved so that successional dynamics are able to occur naturally.

Assessing the threat of bat-associated fungal pathogens

Fungal pathogens have become an increasingly important topic in recent decades. Yet whilst various cankers and blights have gained attention in temperate woodlands and crops, the scope for fungal pathogens of animals and their potential threat has received far less attention. With a shifting climate, the threat from fungal pathogens is predicted to increase in the future, thus understanding the spread of fungi over landscapes as well as taxa that may be at risk is of particular importance. Cave ecosystems provide potential refugia for various fungi, and roosts for bats. With their well vascularized wings and wide-ranging distributions, bats present potential fungal vectors. Furthermore, whilst bat immune systems are generally robust to bacterial and viral pathogens, they can be susceptible to fungal pathogens, particularly during periods of stress such as hibernation. Here we explore why bats are important and interesting vectors for fungi across landscapes and discuss knowledge gaps that require further research.

Microbial diversity patterns in the root zone of two Meconopsis plants on the Qinghai-Tibet Plateau

In the extreme alpine climate of the Qinghai-Tibet Plateau (QTP), plant growth and reproduction are limited by extremely cold temperatures, low soil moisture, and scarce nutrient availability. The root-associated microbiome indirectly promotes plant growth and plays a role in the fitness of plants on the QTP, particularly in Tibetan medicinal plants. Despite the importance of the root-associated microbiome, little is known about the root zone. This study used high-throughput sequencing to investigate two medicinal Meconopsis plants, M. horridula and M. integrifolia, to determine whether habitat or plant identity had a more significant impact on the microbial composition of the roots. The fungal sequences were obtained using ITS-1 and ITS-2, and bacterial sequences were obtained using 16S rRNA. Different microbial patterns were observed in the microbial compositions of fungi and bacteria in the root zones of two Meconopsis plants. In contrast to bacteria, which were not significantly impacted by plant identity or habitat, the fungi in the root zone were significantly impacted by plant identity, but not habitat. In addition, the synergistic effect was more significant than the antagonistic effect in the correlation between fungi and bacteria in the root zone soil. The fungal structure was influenced by total nitrogen and pH, whereas the structure of bacterial communities was influenced by soil moisture and organic matter. Plant identity had a greater influence on fungal structure than habitat in two Meconopsis plants. The dissimilarity of fungal communities suggests that more attention should be paid to fungi-plant interactions.

Negative outcomes of novel trophic interactions along mangrove range edges

Tropicalization is a phenomenon that is changing the structure of ecosystems around the world. Mangrove encroachment is a particular form of tropicalization that may have cascading consequences for resident fauna in subtropical coastal wetlands. There is a knowledge gap regarding the extent of interactions between basal consumers and mangroves along mangrove range edges, and the consequences of these novel interactions for the consumers. This study focuses on the key coastal wetland consumers, Littoraria irrorata (marsh periwinkle) and Uca rapax (mudflat fiddler crabs), and their interactions with encroaching Avicennia germinans (black mangrove) in the Gulf of Mexico, USA. In food preference assays, Littoraria avoided consuming Avicennia and selectively ingested leaf tissue from a common marsh grass, Spartina alterniflora (smooth cordgrass), a preference which has also been previously documented in Uca. The quality of Avicennia as a food source was determined by measuring the energy storage of consumers that had interacted with either Avicennia or marsh plants in the lab and the field. Littoraria and Uca both stored approximately 10% less energy when interacting with Avicennia, despite their different feeding behaviors and physiologies. The negative consequences of mangrove encroachment for these species at the individual level suggest that there may be negative population-level effects as encroachment continues. Many previous studies have documented shifts in floral and faunal communities following mangrove replacement of salt marsh vegetation, but this study is the first to identify physiological responses that may be contributing to these shifts.

Vector communities under global change may exacerbate and redistribute infectious disease risk

Vector-borne parasites may be transmitted by multiple vector species, resulting in an increased risk of transmission, potentially at larger spatial scales compared to any single vector species. Additionally, the different abilities of patchily distributed vector species to acquire and transmit parasites will lead to varying degrees of transmission risk. Investigation of how vector community composition and parasite transmission change over space due to variation in environmental conditions may help to explain current patterns in diseases but also informs our understanding of how patterns will change under climate and land-use change. We developed a novel statistical approach using a multi-year, spatially extensive case study involving a vector-borne virus affecting white-tailed deer transmitted by Culicoides midges. We characterized the structure of vector communities, established the ecological gradient controlling change in structure, and related the ecology and structure to the amount of disease reporting observed in host populations. We found that vector species largely occur and replace each other as groups, rather than individual species. Moreover, community structure is primarily controlled by temperature ranges, with certain communities being consistently associated with high levels of disease reporting. These communities are essentially composed of species previously undocumented as potential vectors, whereas communities containing putative vector species were largely associated with low levels, or even absence, of disease reporting. We contend that the application of metacommunity ecology to vector-borne infectious disease ecology can greatly aid the identification of transmission hotspots and an understanding of the ecological drivers of parasite transmission risk both now and in the future.

Implications of Soil Microbial Community Assembly for Ecosystem Restoration: Patterns, Process, and Potential

While it is now widely accepted that microorganisms provide essential functions in restoration ecology, the nature of relationships between microbial community assembly and ecosystem recovery remains unclear. There has been a longstanding challenge to decipher whether microorganisms facilitate or simply follow ecosystem recovery, and evidence for each is mixed at best. We propose that understanding microbial community assembly processes is critical to understanding the role of microorganisms during ecosystem restoration and thus optimizing management strategies. We examine how the connection between environment, community structure, and function is fundamentally underpinned by the processes governing community assembly of these microbial communities. We review important factors to consider in evaluating microbial community structure in the context of ecosystem recovery as revealed in studies of microbial succession: (1) variation in community assembly processes, (2) linkages to ecosystem function, and (3) measurable microbial community attributes. We seek to empower restoration ecology with microbial assembly and successional understandings that can generate actionable insights and vital contexts for ecosystem restoration efforts.

Plant species composition and local habitat conditions as primary determinants of terrestrial arthropod assemblages

Arthropods respond to vegetation in multiple ways since plants provide habitat and food resources and indicate local abiotic conditions. However, the relative importance of these factors for arthropod assemblages is less well understood. We aimed to disentangle the effects of plant species composition and environmental drivers on arthropod taxonomic composition and to assess which aspects of vegetation contribute to the relationships between plant and arthropod assemblages. In a multi-scale field study in Southern Germany, we sampled vascular plants and terrestrial arthropods in typical habitats of temperate landscapes. We compared independent and shared effects of vegetation and abiotic predictors on arthropod composition distinguishing between four large orders (Lepidoptera, Coleoptera, Hymenoptera, Diptera), and five functional groups (herbivores, pollinators, predators, parasitoids, detritivores). Across all investigated groups, plant species composition explained the major fraction of variation in arthropod composition, while land-cover composition was another important predictor. Moreover, the local habitat conditions depicted by the indicator values of the plant communities were more important for arthropod composition than trophic relationships between certain plant and arthropod species. Among trophic groups, predators showed the strongest response to plant species composition, while responses of herbivores and pollinators were stronger than those of parasitoids and detritivores. Our results highlight the relevance of plant community composition for terrestrial arthropod assemblages across multiple taxa and trophic levels and emphasize the value of plants as a proxy for characterizing habitat conditions that are hardly accessible to direct environmental measurements.

Co-occurrence probabilities between mosquito vectors of West Nile and Eastern equine encephalitis viruses using Markov Random Fields (MRFcov)

Mosquito vectors of eastern equine encephalitis virus (EEEV) and West Nile virus (WNV) in the USA reside within broad multi-species assemblages that vary in spatial and temporal composition, relative abundances and vector competence. These variations impact the risk of pathogen transmission and the operational management of these species by local public health vector control districts. However, most models of mosquito vector dynamics focus on single species and do not account for co-occurrence probabilities between mosquito species pairs across environmental gradients. In this investigation, we use for the first time conditional Markov Random Fields (CRF) to evaluate spatial co-occurrence patterns between host-seeking mosquito vectors of EEEV and WNV around sampling sites in Manatee County, Florida. Specifically, we aimed to: (i) quantify correlations between mosquito vector species and other mosquito species; (ii) quantify correlations between mosquito vectors and landscape and climate variables; and (iii) investigate whether the strength of correlations between species pairs are conditional on landscape or climate variables. We hypothesized that either mosquito species pairs co-occur in patterns driven by the landscape and/or climate variables, or these vector species pairs are unconditionally dependent on each other regardless of the environmental variables. Our results indicated that landscape and bioclimatic covariates did not substantially improve the overall model performance and that the log abundances of the majority of WNV and EEEV vector species were positively dependent on other vector and non-vector mosquito species, unconditionally. Only five individual mosquito vectors were weakly dependent on environmental variables with one exception, Culiseta melanura, the primary vector for EEEV, which showed a strong correlation with woody wetland, precipitation seasonality and average temperature of driest quarter. Our analyses showed that majority of the studied mosquito species' abundance and distribution are insignificantly better predicted by the biotic correlations than by environmental variables. Additionally, these mosquito vector species may be habitat generalists, as indicated by the unconditional correlation matrices between species pairs, which could have confounded our analysis, but also indicated that the approach could be operationalized to leverage species co-occurrences as indicators of vector abundances in unsampled areas, or under scenarios where environmental variables are not informative.

The community ecology perspective of omics data

The measurement of uncharacterized pools of biological molecules through techniques such as metabarcoding, metagenomics, metatranscriptomics, metabolomics, and metaproteomics produces large, multivariate datasets. Analyses of these datasets have successfully been borrowed from community ecology to characterize the molecular diversity of samples (ɑ-diversity) and to assess how these profiles change in response to experimental treatments or across gradients (β-diversity). However, sample preparation and data collection methods generate biases and noise which confound molecular diversity estimates and require special attention. Here, we examine how technical biases and noise that are introduced into multivariate molecular data affect the estimation of the components of diversity (i.e., total number of different molecular species, or entities; total number of molecules; and the abundance distribution of molecular entities). We then explore under which conditions these biases affect the measurement of ɑ- and β-diversity and highlight how novel methods commonly used in community ecology can be adopted to improve the interpretation and integration of multivariate molecular data. Video Abstract.

Alterations of the fecal microbiota in relation to acute COVID-19 infection and recovery

People with acute COVID-19 due to SARS-CoV-2 infection experience a range of symptoms, but major factors contributing to severe clinical outcomes remain to be understood. Emerging evidence suggests associations between the gut microbiome and the severity and progression of COVID-19. To better understand the host-microbiota interactions in acute COVID-19, we characterized the intestinal microbiome of patients with active SARS-CoV-2 infection in comparison to recovered patients and uninfected healthy controls. We performed 16S rRNA sequencing of stool samples collected between May 2020 and January 2021 from 20 COVID-19-positive patients, 20 COVID-19-recovered subjects and 20 healthy controls. COVID-19-positive patients had altered microbiome community characteristics compared to the recovered and control subjects, as assessed by both α- and β-diversity differences. In COVID-19-positive patients, we observed depletion of Bacteroidaceae, Ruminococcaceae, and Lachnospiraceae, as well as decreased relative abundances of the genera Faecalibacterium, Adlercreutzia, and the Eubacterium brachy group. The enrichment of Prevotellaceae with COVID-19 infection continued after viral clearance; antibiotic use induced further gut microbiota perturbations in COVID-19-positive patients. In conclusion, we present evidence that acute COVID-19 induces gut microbiota dysbiosis with depletion of particular populations of commensal bacteria, a phenomenon heightened by antibiotic exposure, but the general effects do not persist post-recovery.

The scale-dependence of spatial distribution of reservoir plankton communities in subtropical and tropical China

Distance-decay relationships (DDRs) represent a very useful approach to describing the spatial distribution of biological communities. However, plankton DDR patterns and community assembly mechanisms are still poorly understood at different spatial scales in reservoir ecosystems. We collected phytoplankton, zooplankton and water samples in 24 reservoirs from subtropical and tropical China from July to August 2018. We examined DDR patterns across three distinct spatial scales, i.e., within-reservoir, within-drainage (but between reservoirs) and between drainages. We tested whether the rate of change (i.e., slope) of DDRs is consistent across different spatial scales. We assessed the relative importance of spatial and environmental variables in shaping the community distribution of plankton and quantitatively distinguished the community assembly mechanisms. We observed significant DDR curves in phytoplankton and zooplankton communities, in which slopes of the DDRs were steepest at the smallest spatial scale. Both spatial and environmental factors had significant impacts on DDR and dispersal assembly was a slightly stronger process in reservoir phytoplankton and zooplankton community assembly than niche-based process. We conclude that DDRs of reservoir phytoplankton and zooplankton vary with spatial scale. Our data shed light on how spatial and environmental variables contribute to plankton community assembly together. However, we revealed that dispersal process contributes to the biogeography of reservoir plankton slightly more strongly than environmental filtering. Collectively, this study enhances the understanding of plankton biogeography and distribution at multiple spatial scales.

NO2 air pollution drives species composition, but tree traits drive species diversity of urban epiphytic lichen communities

Lichens serve as important bioindicators of air pollution in cities. Here, we studied the diversity of epiphytic lichens in the urban area of Munich, Bavaria, southern Germany, to determine which factors influence species composition and diversity. Lichen diversity was quantified in altogether 18 plots and within each, five deciduous trees were investigated belonging to on average three tree species (range 1-5). Of the 18 plots, two were sampled in control areas in remote areas of southern Germany. For each lichen species, frequency of occurrence was determined in 10 quadrats of 100 cm² on the tree trunk. Moreover, the cover percentage of bryophytes was determined and used as a variable to represent potential biotic competition. We related our diversity data (species richness, Shannon index, evenness, abundance) to various environmental variables including tree traits, i.e. bark pH levels and species affiliation and air pollution data, i.e. NO₂ and SO₂ concentrations measured in the study plots. The SO₂ levels measured in our study were generally very low, while NO₂ levels were rather high in some plots. We found that the species composition of the epiphytic lichen communities was driven mainly by NO₂ pollution levels and all of the most common species in our study were nitrophilous lichens. Low NO₂ but high SO₂ values were associated with high lichen evenness. Tree-level lichen diversity and abundance were mainly determined by tree traits, not air pollution. These results confirm that ongoing NO₂ air pollution within cities is a major threat to lichen diversity, with non-nitrophilous lichens likely experiencing the greatest risk of local extinctions in urban areas in the future. Our study moreover highlights the importance of large urban green spaces for species diversity. City planners need to include large green spaces when designing urban areas, both to improve biodiversity and to promote human health and wellbeing.

Pathogens and predators: examining the separate and combined effects of natural enemies on assemblage structure

Natural enemy ecology strives to unify predator-prey and host-pathogen interactions under a common framework to gain insights into community- and ecosystem-level processes. To address this goal, ecologists need a greater emphasis on: (1) quantifying pathogen-mediated effects on community structure to enable comparisons with predator-mediated effects and (2) determining the interactive effects of combined natural enemies on communities. We conducted a mesocosm experiment to assess the individual and combined effects of predators (dragonfly larvae and adult water bugs) and a pathogen (ranavirus) on the abundance and composition of a larval amphibian assemblage. We found that our three natural enemies structured victim assemblages in unique ways, producing distinct assemblages. Additionally, we found that in combination treatments, predators mainly drove assemblage structure such that the assemblages most closely resembled their respective predator treatments. We also found that predators reduced infection prevalence in combination treatments, and that the magnitude of this effect was dependent on predator identity. Compared to virus-alone treatments, the presence of dragonflies and water bugs reduced infection prevalence by 79% and 63%, respectively. Additionally, the presence of dragonflies eliminated ranavirus infection in two species, which demonstrates the prominent role of predators in disease dynamics in this system. Overall, this work demonstrates the importance of considering natural enemies in community ecology, as each enemy can elicit a unique structural change. Additionally, this study provides a unique empirical test of the healthy herds hypothesis for multi-species assemblages and underscores the importance of advancing our understanding of multi-enemy interactions within communities.

Disappearance of an ecosystem engineer, the white-lipped peccary (Tayassu pecari), leads to density compensation and ecological release

Given the rate of biodiversity loss, there is an urgent need to understand community-level responses to extirpation events, with two prevailing hypotheses. On one hand, the loss of an apex predator leads to an increase in primary prey species, triggering a trophic cascade of other changes within the community, while density compensation and ecological release can occur because of reduced competition for resources and absence of direct aggression. White-lipped peccary (Tayassu pecari—WLP), a species that typically co-occurs with collared peccary (Pecari tajacu), undergo major population crashes—often taking 20 to 30-years for populations to recover. Using a temporally replicated camera trapping dataset, in both a pre- and post- WLP crash, we explore how WLP disappearance alters the structure of a Neotropical vertebrate community with findings indicative of density compensation. White-lipped peccary were the most frequently detected terrestrial mammal in the 2006–2007 pre-population crash period but were undetected during the 2019 post-crash survey. Panthera onca (jaguar) camera trap encounter rates declined by 63% following the WLP crash, while collared peccary, puma (Puma concolor), red-brocket deer (Mazama americana) and short-eared dog (Atelocynus microtis) all displayed greater encounter rates (490%, 150%, 280%, and 500% respectively), and increased in rank-abundance. Absence of WLP was correlated with ecological release changes in habitat-use for six species, with the greatest increase in use in the preferred floodplain habitat of the WLP. Surprisingly, community-weighted mean trait distributions (body size, feeding guild and nocturnality) did not change, suggesting functional redundancy in diverse tropical mammal assemblages.

Different temporal trends in vascular plant and bryophyte communities along elevational gradients over four decades

Despite many studies showing biodiversity responses to warming, the generality of such responses across taxonomic groups remains unclear. Very few studies have tested for evidence of bryophyte community responses to warming, even though bryophytes are major contributors to diversity and functioning in many ecosystems. Here, we report an empirical study comparing long‐term change in bryophyte and vascular plant communities in two sites with contrasting long‐term warming trends, using “legacy” botanical records as a baseline for comparison with contemporary resurveys. We hypothesized that ecological changes would be greater in sites with a stronger warming trend and that vascular plant communities, with narrower climatic niches, would be more sensitive than bryophyte communities to climate warming. For each taxonomic group in each site, we quantified the magnitude of changes in species' distributions along the elevation gradient, species richness, and community composition. We found contrasted temporal changes in bryophyte vs. vascular plant communities, which only partially supported the warming hypothesis. In the area with a stronger warming trend, we found a significant increase in local diversity and dissimilarity (β‐diversity) for vascular plants, but not for bryophytes. Presence–absence data did not provide sufficient power to detect elevational shifts in species distributions. The patterns observed for bryophytes are in accordance with recent literature showing that local diversity can remain unchanged despite strong changes in composition. Regardless of whether one taxon is systematically more or less sensitive to environmental change than another, our results suggest that vascular plants cannot be used as a surrogate for bryophytes in terms of predicting the nature and magnitude of responses to warming. Thus, to assess overall biodiversity responses to global change, abundance data from different taxonomic groups and different community properties need to be synthesized.

Ecosystem-specific microbiota and microbiome databases in the era of big data

The rapid development of sequencing methods over the past decades has accelerated both the potential scope and depth of microbiota and microbiome studies. Recent developments in the field have been marked by an expansion away from purely categorical studies towards a greater investigation of community functionality. As in-depth genomic and environmental coverage is often distributed unequally across major taxa and ecosystems, it can be difficult to identify or substantiate relationships within microbial communities. Generic databases containing datasets from diverse ecosystems have opened a new era of data accessibility despite costs in terms of data quality and heterogeneity. This challenge is readily embodied in the integration of meta-omics data alongside habitat-specific standards which help contextualise datasets both in terms of sample processing and background within the ecosystem. A special case of large genomic repositories, ecosystem-specific databases (ES-DB's), have emerged to consolidate and better standardise sample processing and analysis protocols around individual ecosystems under study, allowing independent studies to produce comparable datasets. Here, we provide a comprehensive review of this emerging tool for microbial community analysis in relation to current trends in the field. We focus on the factors leading to the formation of ES-DB's, their comparison to traditional microbial databases, the potential for ES-DB integration with meta-omics platforms, as well as inherent limitations in the applicability of ES-DB's.

Community assembly of microbial habitat generalists and specialists in urban aquatic ecosystems explained more by habitat type than pollution gradient

Urban freshwater ecosystems have important ecosystem functions, provide habitats for diverse microbial communities and are susceptible to multiple interconnected factors such as environmental pollution. Despite the ecological significance of bacteria and microeukaryotes, little is known about how their community assembly responds to various environmental factors across water and sediment habitats and ecological processes shaping them. Here, environmental DNA-based approaches were used to investigate the community assembly processes of bacteria and microeukaryotes (including habitat generalists and specialists) in urban water and sediment across an urban-pollution gradient in Wuhan, central China. The diversity, community composition and potential function of bacteria and microeukaryotes showed significantly stronger variation between water and sediment than across an urban pollution gradient. Although, bacterial and microeukaryotic community assemblies were dominated by strong selection processes in both water and sediment habitats, but a contrasting community assembly mechanism was identified between habitat generalists and specialists. Bacterial and microeukaryotic communities showed a greater response to physicochemical variability in water, while a strong distance-decay relationship was found in sediment. Further, cross-kingdom microbial network analysis revealed strong modular associations of bacteria and microeukaryotes, meanwhile, microeukaryotic habitat specialists might be keystone, but generalists have higher proportion of connections in the networks. This study provides significant insights into the response of bacteria and microeukaryotes to different urban pollutions between water and sediment, and the ecological processes structuring microbial community dynamics across habitat types under anthropogenic disturbances.

Impacts of wastewater treatment plants on benthic macroinvertebrate communities in summer and winter

Treated effluent from municipal wastewater treatment plants (WWTPs) is a major source of contamination that can impact population size, community structure, and biodiversity of aquatic organisms. However, because the majority of field research occurs during warmer periods of the year, the impacts of wastewater effluent on aquatic communities during winter has largely been neglected. In this study, we assessed the impacts of wastewater effluent on aquatic benthic macroinvertebrate (benthos) communities along the effluent gradients of two WWTPs discharging into Hamilton Harbour, Canada, during summer and winter using artificial substrates incubated for 8 weeks. At the larger of the two plants, benthic macroinvertebrate abundance was higher and diversity was lower at sites downstream of the outfall compared to upstream sites in both seasons. Whereas at the smaller plant, the opposite was observed, abundance increased and diversity decreased with distance from the outfall in both seasons. While the impacts of wastewater on benthic communities were largely similar between seasons, we did detect several general seasonal trends - family diversity of macroinvertebrates was lower during winter at both WWTPs and total abundance was also lower during winter, but only significantly so at the smaller WWTP. Further, benthic macroinvertebrate community composition differed significantly along the effluent gradients, with sites closest and farthest from the outfall being the most dissimilar. Our contrasting results between the WWTPs demonstrate that plants, with different treatment capabilities and effluent-receiving environments (industrial/urban versus wetland), can dictate how wastewater effluent impacts benthic macroinvertebrate communities.

MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations

BACKGROUND

Microbes and their viruses are hidden engines driving Earth's ecosystems from the oceans and soils to humans and bioreactors. Though gene marker approaches can now be complemented by genome-resolved studies of inter-(macrodiversity) and intra-(microdiversity) population variation, analytical tools to do so remain scattered or under-developed.

RESULTS

Here, we introduce MetaPop, an open-source bioinformatic pipeline that provides a single interface to analyze and visualize microbial and viral community metagenomes at both the macro- and microdiversity levels. Macrodiversity estimates include population abundances and α- and β-diversity. Microdiversity calculations include identification of single nucleotide polymorphisms, novel codon-constrained linkage of SNPs, nucleotide diversity (π and θ), and selective pressures (pN/pS and Tajima's D) within and fixation indices (FST) between populations. MetaPop will also identify genes with distinct codon usage. Following rigorous validation, we applied MetaPop to the gut viromes of autistic children that underwent fecal microbiota transfers and their neurotypical peers. The macrodiversity results confirmed our prior findings for viral populations (microbial shotgun metagenomes were not available) that diversity did not significantly differ between autistic and neurotypical children. However, by also quantifying microdiversity, MetaPop revealed lower average viral nucleotide diversity (π) in autistic children. Analysis of the percentage of genomes detected under positive selection was also lower among autistic children, suggesting that higher viral π in neurotypical children may be beneficial because it allows populations to better "bet hedge" in changing environments. Further, comparisons of microdiversity pre- and post-FMT in autistic children revealed that the delivery FMT method (oral versus rectal) may influence viral activity and engraftment of microdiverse viral populations, with children who received their FMT rectally having higher microdiversity post-FMT. Overall, these results show that analyses at the macro level alone can miss important biological differences.

CONCLUSIONS

These findings suggest that standardized population and genetic variation analyses will be invaluable for maximizing biological inference, and MetaPop provides a convenient tool package to explore the dual impact of macro- and microdiversity across microbial communities. Video abstract.

Herbivory in a changing climate-Effects of plant genotype and experimentally induced variation in plant phenology on two summer-active lepidopteran herbivores and one fungal pathogen

With climate change, spring warming tends to advance plant leaf-out. While the timing of leaf-out has been shown to affect the quality of leaves for herbivores in spring, it is unclear whether such effects extend to herbivores active in summer. In this study, we first examined how spring and autumn phenology of seven Quercus robur genotypes responded to elevated temperatures in spring. We then tested whether the performance of two summer-active insect herbivores (Orthosia gothica and Polia nebulosa) and infection by a pathogen (Erysiphe alphitoides) were influenced by plant phenology, traits associated with genotype or the interaction between these two. Warm spring temperatures advanced both bud development and leaf senescence in Q. robur. Plants of different genotype differed in terms of both spring and autumn phenology. Plant phenology did not influence the performance of two insect herbivores and a pathogen, while traits associated with oak genotype had an effect on herbivore performance. Weight gain for O. gothica and ingestion for P. nebulosa differed by a factor of 4.38 and 2.23 among genotypes, respectively. Herbivore species active in summer were influenced by traits associated with plant genotype but not by phenology. This suggest that plant attackers active in summer may prove tolerant to shifts in host plant phenology-a pattern contrasting with previously documented effects on plant attackers active in spring and autumn.

Establishment of baseline cytology metrics in nestling American kestrels (Falco sparverius): Immunomodulatory effects of the flame retardant isopropylated triarylphosphate isomers

Avian populations must mount effective immune responses upon exposure to environmental stressors such as avian influenza and xenobiotics. Although multiple immune assays have been tested and applied to various avian species, antibody-mediated immune responses in non-model avian species are not commonly reported due to the lack of commercially available species-specific antibodies. The objectives of the present study were to advance methods for studying wild bird immune responses and to apply these to the evaluation of cytological responses after exposure of American kestrels, Falco sparverius, to a commercial flame retardant mixture containing isopropylated triarylphosphate isomers (ITP). Hatchlings were gavaged daily with safflower oil or 1.5 ug/g bw/day of ITP suspended in safflower oil, then bled on days 9, 17, and 21. The ITP treatment group (n = 18) and a subset of controls (Poly I:C treatment group; n = 10) were injected on days 9 and 15 with a synthetic analog of viral double-stranded RNA, polyinosinic:polycytidylic acid (Poly I:C), a toll-like receptor ligand and synthetic viral mimic, and responses compared to a sham injected control group (n = 8). The hypotheses tested whether kestrels showed immunological differences among treatment groups, genetic sex, and/or white blood cell (WBC) subpopulation type over time. A flow cytometry (FCM) gating strategy categorized heterophils (H), lymphocytes (L), and monocytes (M) and their proportions, and measured relative fluorescence in response to anti-chicken CD4 binding. Fluorescent cell surfaces and some granular/vacuolar inclusions were visualized by epifluorescence microscopy. A fourth subpopulation with higher levels of granularity than M but less than H became increasingly apparent with time and was gated along with the H subpopulation; its frequency of occurrence was lowest in the ITP group (P = 0.0023). The percentages of cells differed among treatment groups, days, and sexes (P = 0.0001). For both sexes, percentages of H and L were higher than M in control and Poly I:C. In the ITP group, L percentages were higher than H and M (P = 0.0457), and H and L were higher than M on days 9 and 21 (P = 0.0001). The ratios of H:L and H:WBC, indicators of robust immunity, were also higher on days 9 and 21 than on 17 (P = 0.0079). For each sex, the highest levels of activity measured by FCM geometric means (GEO) of fluorescence (indicative of antibody binding) were observed on day 9 (P = 0.0001 female, and P = 0.0011 male) in H over both L and M (P < 0.0001 for each). In males, GEO of the Poly I:C group was higher than that of the ITP group (P = 0.0374), with no difference observed among females over all days. By using a FCM algorithm for population comparisons of fluorescence to investigate binding within H, the T(x) scores indicated higher fluorescence in control and Poly I:C groups over ITP (P = 0.0001). Unlike chickens, Gallus gallus, which express CD4 primarily on L, kestrels bound the commercial antibody primarily within the gated H subpopulation, suggesting an immunophenotypic difference between taxa, despite a ~60% identity of Falco CD4 amino acid sequences with chicken CD4. The emergent cell subset within the gated H presented dendritic-like cell (DLC) morphological and functional properties, apparently serving as an effector cell. This study adds interpretive context to ecological investigations of infection and of potential immunomodulation by emerging compounds, whereby the early innate responses are mediated by the various cell subsets serving as useful quantitative markers of immunological condition. Data showed that dietary exposure to ITP was immunosuppressive for male and female kestrels over the course of the experiment, reducing DLC frequency compared to the Poly I:C controls. Heterophils and DLC were important in facilitating innate immunological responses.

Ecological and Metabolic Thresholds in the Bacterial, Protist, and Fungal Microbiome of Ephemeral Saline Lakes (Monegros Desert, Spain)

We studied the 16S and 18S rRNA genes of the bacterial, protist, and fungal microbiomes of 131 samples collected in 14 ephemeral small inland lakes located in the endorheic area of the Monegros Desert (NE Spain). The sampling covered different temporal flooding/desiccation cycles that created natural salinity gradients between 0.1% (w/v) and salt saturation. We aimed to test the hypothesis of a lack of competitive advantage for microorganisms using the "salt-in" strategy in highly fluctuating hypersaline environments where temperature and salinity transitions widely vary within short time periods, as in ephemeral inland lakes. Overall, 5653 bacterial zOTUs and 2658 eukaryal zOTUs were detected heterogeneously distributed with significant variations on taxonomy and general energy-yielding metabolisms and trophic strategies along the gradient. We observed a more diverse bacterial assembly than initially expected at extreme salinities and a lack of dominance of a few "salt-in" organisms. Microbial thresholds were unveiled for these highly fluctuating hypersaline environments with high selective pressures. We conclude that the extremely high dynamism observed in the ephemeral lakes of Monegros may have given a competitive advantage for more versatile ("salt-out") organisms compared to those better adapted to stable high salinities usually more common in solar salterns. Ephemeral inland saline lakes offered a well-suited natural framework for highly detailed evolutionary and ecological studies.

Effects of ticks on community assemblages of ectoparasites in deer mice

Ectoparasites are fundamental to ecosystems, playing a key role in trophic regulation. Fleas, mites, and ticks are common hematophagous ectoparasites that infest shared mammalian hosts. One common host in Ontario, Canada, is the deer mouse (Peromyscus maniculatus). As the climate warms and the geographic ranges of blacklegged ticks (Ixodes scapularis) and American dog ticks (Dermacentor variabilis) expand, their introduction to new ecosystems may alter current ectoparasite communities. At three different sites where exposure to ticks varied (both in terms of tick diversity and abundance), ectoparasite community structures found on deer mouse hosts were examined, focusing on species co-occurrences and habitat partitioning on the host. We predicted that when tick species were prevalent, ticks would dominate the micro-habitat attachment sites often inhabited by other parasites, thereby significantly altering parasite community structure. Our results suggest that blacklegged ticks and American dog ticks could have a positive association with each other, but a negative or random association with other ectoparasite species, even when they do not occupy the same attachment site. Sampling site played a significant role in community assemblages as well, possibly due to the differences in tick exposure. As the ticks' ranges expand and they become more abundant, it is important to understand how their prevalence can potentially alter the dynamics in an ectoparasite community, affecting the transmission of pathogens that may spread within an ecosystem, from one host to another.

The rise of ecological parasitology: twelve landmark advances that changed its history

In the five decades since the first publication of the International Journal for Parasitology, ecological parasitology has grown from modest beginnings to become a modern discipline with a strong theoretical foundation, a diverse toolkit, and a multidisciplinary approach. In this review, I highlight 12 advances in the field that have spurred its growth over the past 50 years. Where relevant, I identify pivotal contributions that have altered the course of research, as well as the influence of developments in other fields such as mainstream ecology and molecular biology. The 12 key advances discussed are in areas including parasite population dynamics and community assembly, the regulation of host population abundance and food web structure, parasites as agents of natural selection, the impacts of biodiversity and anthropogenic changes on host-parasite interactions, the biogeography of parasite diversity, and the evolutionary genetics of parasites. I conclude by identifying some challenges and opportunities lying ahead, which need to be met for the future growth of ecological research on host-parasite interactions.

Temperature and productivity distinctly affect the species richness of ectothermic and endothermic multitrophic guilds along a tropical elevational gradient

The diversity of endotherms and ectotherms may be differently affected by ambient temperature and net primary productivity (NPP). Additionally, little is known about how these drivers affect the diversity of guilds of different trophic levels. We assessed the relative role of temperature and NPP in multitrophic guilds of ectothermic (arthropods: ants, ground beetles, spiders, and harvestmen) and endothermic (large mammals) animals along a tropical elevational gradient. We sampled arthropods at eight elevation belts and large mammals at 14 elevation belts in Atlantic rainforest (ranging from 600 to 2450 m.a.s.l.) of Itatiaia National Park, Southeast Brazil. Overall arthropod species richness was more associated with temperature than overall large-mammal species richness, while the latter was more associated with NPP. When separated into trophic guilds, we found that the species richness associated with NPP increased across arthropod trophic levels from herbivores to predators. Conversely, although NPP influenced large-mammal herbivore species richness, its effects did not seem to accumulate across large-mammal trophic levels since the species richness of large-mammal omnivores was more associated with temperature and none of the variables we studied influenced large-mammal predators. We suggest that thermal physiological differences between ectotherms and endotherms are responsible for the way in which arthropods and large mammals interact with or are constrained by the environment. Furthermore, the inconsistency regarding the role of temperature and NPP on species richness across multitrophic guilds of ectotherms and endotherms could indicate that thermal physiological differences might also interfere with energy use and flux in the food web.

Merging Fungal and Bacterial Community Profiles via an Internal Control

Integrated measurements of fungi and bacteria are critical to understand how interactions between these taxa drive key processes in ecosystems ranging from soils to animal guts. High-throughput amplicon sequencing is commonly used to census microbiomes, but the genetic markers targeted for fungi and bacteria (typically ribosomal regions) are domain-specific so profiling must be performed separately, obscuring relationships between these groups. To solve this problem, we developed a spike-in method with an internal control (IC) construct containing primer sites commonly used for bacterial and fungal taxonomic profiling. The internal control offers several advantages: estimation of absolute abundances, estimation of fungal to bacterial ratios (F:B), integration of bacterial and fungal profiles for holistic community analysis, and lower costs compared to other quantitation methods. To validate the IC as a scaling method, we compared IC-derived measures of F:B to measures from quantitative PCR (qPCR) using a commercial mock community (the ZymoBiomic Microbial Community DNA Standard II, containing two fungi and eight bacteria) and complex environmental samples. For both the mock community and the environmental samples, the IC produced F:B values that were statistically consistent with qPCR. Merging the environmental fungal and bacterial profiles based on the IC-derived F:B values revealed new relationships among samples in terms of community similarity. This IC method is the first spike-in method to employ a single construct for cross-domain amplicon sequencing, offering more reliable measurements.

Altered precipitation and root herbivory affect the productivity and composition of a mesic grassland

BACKGROUND

Climate change models predict changes in the amount, frequency and seasonality of precipitation events, all of which have the potential to affect the structure and function of grassland ecosystems. While previous studies have examined plant or herbivore responses to these perturbations, few have examined their interactions; even fewer have included belowground herbivores. Given the ecological, economic and biodiversity value of grasslands, and their importance globally for carbon storage and agriculture, this is an important knowledge gap. To address this, we conducted a precipitation manipulation experiment in a former mesic pasture grassland comprising a mixture of C₄ grasses and C₃ grasses and forbs, in southeast Australia. Rainfall treatments included a control [ambient], reduced amount [50% ambient] and reduced frequency [ambient rainfall withheld for three weeks, then applied as a single deluge event] manipulations, to simulate predicted changes in both the size and frequency of future rainfall events. In addition, half of all experimental plots were inoculated with adult root herbivores (Scarabaeidae beetles).

RESULTS

We found strong seasonal dependence in plant community responses to both rainfall and root herbivore treatments. The largest effects were seen in the cool season with lower productivity, cover and diversity in rainfall-manipulated plots, while root herbivore inoculation increased the relative abundance of C₃, compared to C₄, plants.

CONCLUSIONS

This study highlights the importance of considering not only the seasonality of plant responses to altered rainfall, but also the important role of interactions between abiotic and biotic drivers of vegetation change when evaluating ecosystem-level responses to future shifts in climatic conditions.

Low shifts in salinity determined assembly processes and network stability of microeukaryotic plankton communities in a subtropical urban reservoir

BACKGROUND

Freshwater salinization may result in significant changes of microbial community composition and diversity, with implications for ecosystem processes and function. Earlier research has revealed the importance of large shifts in salinity on microbial physiology and ecology, whereas studies on the effects of smaller or narrower shifts in salinity on the microeukaryotic community in inland waters are scarce. Our aim was to unveil community assembly mechanisms and the stability of microeukaryotic plankton networks at low shifts in salinity.

RESULTS

Here, we analyzed a high-resolution time series of plankton data from an urban reservoir in subtropical China over 13 consecutive months following one periodic salinity change ranging from 0 to 6.1‰. We found that (1) salinity increase altered the community composition and led to a significant decrease of plankton diversity, (2) salinity change influenced microeukaryotic plankton community assembly primarily by regulating the deterministic-stochastic balance, with deterministic processes becoming more important with increased salinity, and (3) core plankton subnetwork robustness was higher at low-salinity levels, while the satellite subnetworks had greater robustness at the medium-/high-salinity levels. Our results suggest that the influence of salinity, rather than successional time, is an important driving force for shaping microeukaryotic plankton community dynamics.

CONCLUSIONS

Our findings demonstrate that at low salinities, even small increases in salinity are sufficient to exert a selective pressure to reduce the microeukaryotic plankton diversity and alter community assembly mechanism and network stability. Our results provide new insights into plankton ecology of inland urban waters and the impacts of salinity change in the assembly of microbiotas and network architecture. Video abstract.

Relative importance of tree species richness, tree functional type, and microenvironment for soil macrofauna communities in European forests

Soil fauna communities are major drivers of many forest ecosystem processes. Tree species diversity and composition shape soil fauna communities, but their relationships are poorly understood, notably whether or not soil fauna diversity depends on tree species diversity. Here, we characterized soil macrofauna communities from forests composed of either one or three tree species, located in four different climate zones and growing on different soil types. Using multivariate analysis and model averaging we investigated the relative importance of tree species richness, tree functional type (deciduous vs. evergreen), litter quality, microhabitat and microclimatic characteristics as drivers of soil macrofauna community composition and structure. We found that macrofauna communities in mixed forest stands were represented by a higher number of broad taxonomic groups that were more diverse and more evenly represented. We also observed a switch from earthworm-dominated to predator-dominated communities with increasing evergreen proportion in forest stands, which we interpreted as a result of a lower litter quality and a higher forest floor mass. Finally, canopy openness was positively related to detritivore abundance and biomass, leading to higher predator species richness and diversity probably through trophic cascade effects. Interestingly, considering different levels of taxonomic resolution in the analyses highlighted different facets of macrofauna response to tree species richness, likely a result of both different ecological niche range and methodological constraints. Overall, our study supports the positive effects of tree species richness on macrofauna diversity and abundance through multiple changes in resource quality and availability, microhabitat, and microclimate modifications.

How political philosophies can help to discuss and differentiate theories in community ecology

This paper uses structural analogies to competing political philosophies of human society as a heuristic tool to differentiate between ecological theories and to bring out new aspects of apparently well-known classics of ecological scholarship. These two different areas of knowledge have in common that their objects are 'societies', i.e. units composed of individuals, and that contradictory and competing theories about these supra-individual units exist. The benefit of discussing ecological theories in terms of their analogies to political philosophies, in this case liberalism, democratism and conservatism, consists in the fact that political philosophies show clear differences and particularities as regards their approach to the concepts of individuality and intentional action. The method therefore helps to expose peculiarities of ecological theories that are usually considered canonical (e.g. Clements, Gleason), as well as hybrid forms (E. P. Odum), and to differentiate between two different types of theories about functional wholes. The basis of this method is the constitutional-theoretical premise that modern paradigms of socialization structure the ecological discourse.

Changes in the analysis of temporal community dynamics data: a 29-year literature review

BACKGROUND

Understanding how biological communities change over time is of increasing importance as Earth moves into the Anthropocene. A wide variety of methods are used for multivariate community analysis and are variously applied to research that aims to characterise temporal dynamics in community composition. Understanding these methods and how they are applied is useful for determining best practice in community ecology.

METHODOLOGY

We reviewed the ecological literature from 1990 to 2018 that used multivariate methods to address questions of temporal community dynamics. For each paper that fulfilled our search criteria, we recorded the types of multivariate analysis used to characterise temporal community dynamics in addition to the research aim, habitat type, location, taxon and the experimental design.

RESULTS

Most studies had relatively few temporal replicates; the median number was seven time points. Nearly 70% of studies applied more than one analysis method; descriptive methods such as bar graphs and ordination were the most commonly applied methods. Surprisingly, the types of analyses used were only related to the number of temporal replicates, but not to research aim or any other aspects of experimental design such as taxon, or habitat or year of study.

CONCLUSIONS

This review reveals that most studies interested in understanding community dynamics use relatively short time series meaning that several, more sophisticated, temporal analyses are not widely applicable. However, newer methods using multivariate dissimilarities are growing in popularity and many can be applied to time series of any length.